System parameters optional files
Two files—a LUS data file and a user-defined Stutter file—are optional for estimating system parameters in MaSTR.
LUS data file: A LUS data file details the longest uninterrupted stretches for the alleles. The file is a text (*.txt) file and it is specific for the panel that was used to analyze the single source validation data. The file must adhere to the following format requirements:
The file must be in *.json format.
The top level in the file is a dictionary.
The top level keys are marker names.
The top level values are dictionaries with the Key = Allele and the Value = Longest uninterrupted sequence with all alleles taken from the common alleles found in the NIST STR database (STRBase).
LUS data file example
A user-defined Stutter file. By default, MaSTR calculates stutter as -1 repeat for all markers. Some markers, however, have different stutter values such as +1 repeat, +/- 1/2 repeat, and so on. A user-defined Stutter file is a text (*.txt) file that details these different stutter values and it is specific for the panel that was used to analyze the single source validation data. The file must adhere to the following format requirements:
The file must have a Header line.
The file must use a comma (,) as a delimiter.
The file must be in *.csv format.
Each row must have exactly four columns.
The ratio must be a decimal value that falls between 0.0 and 1.0.
The From Allele and the To Allele must use valid allele names; for example, OB is not an allowed value.
An allele name must use the standard naming format, for example, 15.2, where the integer portion represents whole repeats and the decimal portion represents partial base repeats. For example, 15.2 represents 15 repeats and an additional 2 bp.
The file cannot use a pound symbol (#) to skip lines.
The file cannot have empty new lines between rows.
The file can have a single trailing newline (\n) for compatibility.
User-defined stutter file example